Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF SHEWANELLA ONEIDENSIS NRTR COMPLEXED WITH A 27MER DNA
 
Authors :  N. Huang, H. Zhang
Date :  06 Apr 09  (Deposition) - 09 Jun 09  (Release) - 28 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Dna Binding Protein, Nudix Domain, Whth Domain, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Huang, J. De Ingeniis, L. Galeazzi, C. Mancini, Y. D. Korostelev, A. B. Rakhmaninova, M. S. Gelfand, D. A. Rodionov, N. Raffaelli, H. Zhang
Structure And Function Of An Adp-Ribose-Dependent Transcriptional Regulator Of Nad Metabolism
Structure V. 17 939 2009
PubMed-ID: 19604474  |  Reference-DOI: 10.1016/J.STR.2009.05.012
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MUTT/NUDIX FAMILY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NRTR, SO_1979
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 70863
 
Molecule 2 - DNA (27-MER)
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (27-MER)
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:87 , LEU B:87BINDING SITE FOR RESIDUE NA A 238

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GZ6)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1His A:44 -Pro A:45
2Glu A:169 -Pro A:170
3His B:44 -Pro B:45
4Glu B:169 -Pro B:170

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GZ6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GZ6)

(-) Exons   (0, 0)

(no "Exon" information available for 3GZ6)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:219
 aligned with Q8EFJ3_SHEON | Q8EFJ3 from UniProtKB/TrEMBL  Length:237

    Alignment length:219
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227         
         Q8EFJ3_SHEON    18 QLLTVDAVLFTYHDQQLKVLLVQRSNHPFLGLWGLPGGFIDETCDESLEQTVLRKLAEKTAVVPPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQACQIQIASVSDVKWWPLADVLQMPLAFDHLQLIEQARERLTQKALYSLVPGFALSEPFTLPELQHVHEVLLGKPIQGKSFRRRVEQADLLIDTGLKRTERGRPANLYCLKPDTASYRFLRNLE 236
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....eeeeeee.........ee..ee........hhhhhhhhhhhhhhh....eeeeeeeeee........eeeeeeeee..hhhhhhhhhh...eeeeehhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhh.eeeeeeee......eeeeee.hhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gz6 A  18 QLLTVDAVLFTYHDQQLKVLLVQRSNHPFLGLWGLPGGFIDETCDESLEQTVLRKLAEKTAVVPPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQACQIQIASVSDVKWWPLADVLQMPLAFDHLQLIEQARERLTQKALYSLVPGFALSEPFTLPELQHVHEVLLGKPIQGKSFRRRVEQADLLIDTGLKRTERGRPANLYCLKPDTASYRFLRNLE 236
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227         


Chain B from PDB  Type:PROTEIN  Length:219
 aligned with Q8EFJ3_SHEON | Q8EFJ3 from UniProtKB/TrEMBL  Length:237

    Alignment length:219
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227         
         Q8EFJ3_SHEON    18 QLLTVDAVLFTYHDQQLKVLLVQRSNHPFLGLWGLPGGFIDETCDESLEQTVLRKLAEKTAVVPPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQACQIQIASVSDVKWWPLADVLQMPLAFDHLQLIEQARERLTQKALYSLVPGFALSEPFTLPELQHVHEVLLGKPIQGKSFRRRVEQADLLIDTGLKRTERGRPANLYCLKPDTASYRFLRNLE 236
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....eeeeeee.........ee..eee.......hhhhhhhhhhhhhhh....eeeeeeeeee........eeeeeeeee..hhhhhhhhhh...eeeeehhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh...hhhhhhhhhhhhh.eeeeeeee......eeeeee.hhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gz6 B  18 QLLTVDAVLFTYHDQQLKVLLVQRSNHPFLGLWGLPGGFIDETCDESLEQTVLRKLAEKTAVVPPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQACQIQIASVSDVKWWPLADVLQMPLAFDHLQLIEQARERLTQKALYSLVPGFALSEPFTLPELQHVHEVLLGKPIQGKSFRRRVEQADLLIDTGLKRTERGRPANLYCLKPDTASYRFLRNLE 236
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227         


Chain C from PDB  Type:DNA  Length:27
                                                           
                 3gz6 C   1 GTAATAGTGTCTTAAAGACACTATTAC  27
                                    10        20       


Chain D from PDB  Type:DNA  Length:27
                                                           
                 3gz6 D   1 GTAATAGTGTCTTTAAGACACTATTAC  27
                                    10        20
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3GZ6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GZ6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GZ6)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8EFJ3_SHEON | Q8EFJ3)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:169 - Pro A:170   [ RasMol ]  
    Glu B:169 - Pro B:170   [ RasMol ]  
    His A:44 - Pro A:45   [ RasMol ]  
    His B:44 - Pro B:45   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3gz6
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q8EFJ3_SHEON | Q8EFJ3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q8EFJ3_SHEON | Q8EFJ3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q8EFJ3_SHEON | Q8EFJ3: 3gz5 3gz8

(-) Related Entries Specified in the PDB File

3gz5 3gz8